|
| Status |
Public on Feb 03, 2023 |
| Title |
T3, Intestine, TRDKO; rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestine
|
| Organism |
Xenopus tropicalis |
| Characteristics |
tissue: Intestine
developmental stage: tadpoles at stage 54
genotype: TRDKO
treatment: T3 treatment
|
| Treatment protocol |
Wild-type and TRDKO tadpoles at stage 54 treated with or without 5 nM T3 at 25°C for 18 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy® Mini Kit 250 (QIAGEN). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
IN_TRDKOT3_1
|
| Data processing |
Raw read sequence were trimmed with cutadapt 3.2 to remove adapter sequence.
Trimmed reads were mapped to genome with STAR 2.7.7a.
Mapped reads were counted with featureCounts from subread 2.0.1.
Assembly: Xenopus_tropicalis (Xenbase v10.0)
Supplementary files format and content: featurecounts_by_gene_name.txt: Tab-delimited text file with read counts for each gene.
|
| |
|
| Submission date |
Aug 03, 2022 |
| Last update date |
Mar 16, 2023 |
| Contact name |
Ryan Dale |
| E-mail(s) |
dalerr@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Child Health and Human Development
|
| Lab |
Bioinformatics and Scientific Programming Core
|
| Street address |
Rm 10D39, 10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL30018 |
| Series (1) |
| GSE210456 |
Comparative analysis of transcriptome profiles reveals organ-dependent (Intestine and Tail) genomic and nongenomic actions of thyroid hormone in Xenopus tropicalis tadpoles |
|
| Relations |
| BioSample |
SAMN30125055 |
| SRA |
SRX16816170 |
